Creating a gene list using the Venn Diagram

The List Manager can be used to generate lists of genes by applying criteria such as fold change and false discovery rate (FDR) adjusted p-value thresholds.

Select the Analysis tab
Select ANOVAResults in the spreadsheet tree
Select Create Gene List from the Analysis section of the Gene Expression workflow (Figure 1)

Figure 1. Selecting Create Gene List from the Gene Expression workflow

Select E2 vs. Control from the Contrast panel of the ANOVA Streamlined tab in the List Manager dialog
Deselect the Include size of the change option
Set p-value with FDR < to 0.1 (Figure 2)

Figure 2. Configuring the List Manager using the ANOVA Streamlined filtering options

There should be ~545 probe(sets)/genes that meet this threshold.

Select Create

A new spreadsheet, E2 vs. Control, will be added as a child spreadsheet of Breast_Cancer.txt.

Repeat the steps listed above to create lists for E2+ICI vs. Control (~24 genes), E2+Ral vs. Control (~22 genes), and E2+TOT vs. Control (~177 genes) with the same threashold

Now we can use the Venn Diagram to create a list of genes that are differentially regulated in all treatment groups.

Select the Venn Diagram tab in the List Manager dialog

The Venn Diagram shows overlap between selected gene lists.

Select the four created lists (E-H) in the spreadsheet list in the List Manager dialog by selecting each while holding the Ctrl key on your keyboard

The Venn Diagram will display the number of overlapping and distinct genes from the four lists (Figure 3).

Figure 3. Viewing the Venn Diagram with intersections of four lists of significant genes

The intersection of the four ellipses shows that 14 differentially regulated genes are in common between the four threatment schemes.

Select the region intersecting all four ellipses
Right-click the intersected region
Select Create List From Highlighted Regions
Select Close to exit the List Manager dialog

The new list will appear in the spreadsheet tree with a temporary file name (ptpm).

Select the temporary list in the spreadsheet tree
Select () from the command bar
Save the list as fourtreatments

« Removing batch effects Hierarchical clustering using a gene list »

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